Colin Kaepernick vs. Alex Smith: Who Should Start at QB for the 49ers and Why?

The San Francisco 49ers have a legitimate quarterback controversy on their hands, and thanks to his post-game comments, head coach Jim Harbaugh does not possess an easy avenue to a solution.

But if Alex Smith is healthy for the 49ers' Week 12 game against the New Orleans Saints, Harbaugh should make the unpopular decision and continue starting the veteran over second-year quarterback Colin Kaepernick. While easy to get lost in the perfection of Kaepernick in Monday night's 32-7 win over the Chicago Bears, Smith is still a captain who led this same team to the doorstep of the Super Bowl last season.

Injury, not performance, led to this discussion for Smith. The former No. 1 pick is playing well in 2012.

The sample size for Kaepernick is also too small to make a season-long forecast, especially into the postseason. Making a switch now changes the dynamic not only for Week 12, but also the rest of the 2012 season and beyond. There's no going back for Harbaugh if Kaepernick is the pick.

Judging by his post-game comments, however, it's clear that Harbaugh seemed—at least in that moment—to be leaning towards Kaepernick over Smith.

Given the perfect chance to announce he was sticking with Smith as his starter if healthy, Harbaugh instead opened the door for Kaepernick to start in Week 12 against the Saints.

"We'll see," Harbaugh said, according to the AP. "I usually tend to go with the guy that has the hot hand and we have two quarterbacks that have a hot hand."

And just like that, the face of the 49ers poured gasoline on a fire that was already burning hot following Kaepernick's near-flawless performance against the NFL's No. 2 overall defense.

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Of course, this is not to dump water on Kaepernick's first ever NFL start. Given a perfect game plan to attack the Bears, Kaepernick executed it perfectly. He made every throw, was unafraid to attack the Bears downfield and mostly singlehandedly gave the 49ers a 20-0 cushion in the first half.

Kaepernick finished 16-of-23 for 243 yards and two scores. His passer rating was 133.5 and his QBR was 97.5.

As Harbaugh said post game, everything Kaepernick did was "exemplary."

But despite the heroics, the 49ers should still stick with Smith for the rest of the 2012 season.

Let's not forget that Smith is 19-5-1 in the regular season since Harbaugh arrived in San Francisco, including a 13-3 mark in 2011 and a 6-2-1 record this season. Smith also led the 49ers to the NFC Championship after coming back to beat the Saints in a wild and dramatic first-round playoff game last January.

Smith's success from last season—when he threw 17 touchdowns against just five interceptions—has also carried over to 2012. He's more than just a game manager.

Through nine games this season, Smith has completed 70 percent of his passes (first in the NFL) with only five interceptions and a passer rating of 104.1 (third).

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Does that profile not buy Smith any leeway, even against a guy the 49ers moved up to get in the second round two Aprils ago? Is the leash this short that an unfortunate concussion ends everything Smith worked his way up to?

And what kind of message does this send to the 49ers locker room? A team captain, who played well prior to his injury, losing his job over one week? Such a decision could have a negative trickle-down effect.

How quickly some can also forget a more flawless performance from Smith just a few weeks prior.

Facing the Arizona Cardinals—a pass defense allowing less yards and a worse completion percentage than the Bears in 2012—Smith completed 18-of-19 passes for 232 yards and three touchdowns on the road. His passer rating was 157.1, points shy of perfection.

If Alex Smith is healthy, who should start at QB in Week 12 against the New Orleans Saints?

Alex SmithColin KaepernickSubmit Votevote to see results

If Alex Smith is healthy, who should start at QB in Week 12 against the New Orleans Saints?

Alex Smith

56.3%

Colin Kaepernick

43.7%

Total votes: 394

Coming off the bye, Smith then completed seven of his first eight passes for 72 yards and a touchdown before a helmet-to-helmet hit knocked him out of a game that the 49ers went on to tie with Kaepernick under center.

An injury doesn't change what Smith has accomplished over the last 25 games in San Francisco.

And going with Kaepernick now means Harbaugh is essentially stuck with him the rest of the season. Making the switch back to Smith is no longer an option once you make this decision. Is Kaepernick ready to lead this team to the Super Bowl, like Smith almost did a year ago?

Certainly, Kaepernick played well enough to earn himself another start. But Harbaugh is the one who accelerated this controversy, and now he's stuck with a very difficult decision.

Is pulling the rug from underneath Smith, a team leader and captain, who has paid his dues and helped revive the 49ers from obscurity, an intelligent move for now and long term? Conventional wisdom says no.

If Smith is healthy, Harbaugh has a very important decision for the future of his franchise coming up this week. Sitting the former No. 1 pick will have ripple effects for now, the postseason and the 2013 regular season.

While starting Smith over Kaepernick will be an unpopular decision for always-living-in-the-moment fans, it's the choice Harbaugh needs to make for the betterment of his football team.